Hello,
I am trying to translate the amber topology for a system membrane+protein (dry)
to Gromacs. In view of the problems caused in amb2gmx.pl due to the size of the
system (more than 600.000 atoms) I had tried another alternative:
I created the amber topology for the protein and for a unique lipid molecule
separately and I converted them to gromacs using amb2gmx.pl (now, no problems
were found, as is logic). Then, from the gromacs topologies, I construct the
.itp files for the protein and lipid, removing the correspondent lines and
putting them into another file that I have called amberff.itp
However, several atomtypes for the lipid are the same than those for the
protein, and they have nothing to do between them:
[ atomtypes ];name bond_type mass charge ptype sigma
epsilonO O 0.0000 0.0000 A 2.95992e-01 8.78640e-01H1
H1 0.0000 0.0000 A 2.64953e-01 6.56888e-02N3 N3
0.0000 0.0000 A 3.25000e-01 7.11280e-01O2 O2 0.0000
0.0000 A 2.95992e-01 8.78640e-01HA HA 0.0000 0.0000 A
2.64953e-01 6.56888e-02HC HC 0.0000 0.0000 A 2.64953e-01
6.56888e-02C C 0.0000 0.0000 A 3.39967e-01 3.59824e-01CT
CT 0.0000 0.0000 A 3.39967e-01 4.57730e-01HP HP
0.0000 0.0000 A 2.64953e-01 6.56888e-02
and I am getting errors in grompp due to this fact.
Does anybody has any idea to solve this?
Thank you very much for your help in advance.
Rebeca García Fandiño
Parc Cientific de Barcelona
[EMAIL PROTECTED]
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